Changes for page Using JupyterHub in HDC
Last modified by Dennis Segebarth on 2024/10/02 18:14
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... ... @@ -313,85 +313,7 @@ 313 313 Yes 314 314 ))) 315 315 316 -== Downloading Project Data to JupyterHub using the Pilot Command Line Interface == 317 317 318 -After logging into the Pilot Command Line Interface, you can download data from the Project Core into the JupyterHub environment to start your data analyses. 319 319 320 -File related commands are grouped in the {{code}}file{{/code}} category. To view the full list of commands in this category, type {{code}}pilotcli file --help{{/code}}. To download project data, use the file sync command. To view the full list of commands in this category, type {{code}}pilotcli file sync --help{{/code}}. 321 321 322 322 323 -{{code language="none"}} 324 -collaborator4@jupyter-collaborator4:~$ pilotcli file sync --help 325 -Usage: pilotcli file sync [OPTIONS] [PATHS]... OUTPUT_PATH 326 - 327 - Download files/folders from a given Project/folder/file in core zone. 328 - 329 -Options: 330 - -z, --zone TEXT Target Zone (i.e., core/greenroom) 331 - --zip Download files as a zip. 332 - -i, --geid Enable downloading by geid. 333 - --help Show this message and exit. 334 -{{/code}} 335 - 336 -=== Example === 337 - 338 -Downloading a file from the Core to your Home Directory: 339 - 340 -Reminder: Please follow Linux conventions for file management. If your filename contains spaces, wrap it in single or double quotes. 341 - 342 -* //Filename~:// “Chemical Tracking Data.csv” 343 -* //Source~:// Project “Indoc Test Project”, “Core” storage zone, folder “collaborator4” {{code}}indoctestproject/collaborator4/Chemical Tracking Data.csv -z core{{/code}} 344 -* //Destination: //user's Home directory in the Guacamole or JupyterHub VM {{code}}.{{/code}} 345 -* //Command group/option: //{{code}}file sync{{/code}} 346 - 347 -{{code language="none"}} 348 -collaborator4@jupyter-collaborator4:~$ pilotcli file sync indoctestproject/collaborator4/'Chemical Tracking Data.csv' . -z core 349 -start downloading... 350 -Downloading Chemical Tracking Data.csv |██████████████████████████████ 100% 00:00 351 -File has been downloaded successfully and saved to: ./Chemical Tracking Data.csv 352 -{{/code}} 353 - 354 -To confirm successful download, type {{code}}ls{{/code}} and verify the file "Chemical Tracking Data.csv" is stored in the Home folder. 355 - 356 -{{code language="none"}} 357 -collaborator4@jupyter-collaborator4:~$ ls 358 -'Chemical Tracking Data.csv' pilotcli 359 -{{/code}} 360 - 361 -The file “Chemical Tracking Data.csv” can be viewed in the JupyterHub graphical user interface: 362 - 363 -[[image:Jupyter downloaded file in Home folder v2.4.11 2023-05-25 1850.png||height="15%" width="50%"]] 364 - 365 - 366 -== Uploading Project Data from JupyterHub using the Pilot Command Line Interface == 367 - 368 -After analyzing Project data inside the JupyterHub, you can upload the generated outputs back into the Project via the Pilot Command Line Interface. 369 - 370 -=== Example === 371 - 372 -* //Filename//: Chemical Tracking Data rev.csv 373 -* //Source~:// user's Home directory in JupyterHub {{code}}.{{/code}} 374 -* //Destination//: Project “Indoc Test Project”, folder “collaborator4”, “Core” storage zone, 375 -{{code}}indoctestproject/collaborator4{{/code}} {{code}}-z core{{/code}} 376 -* //Command group/option~:// {{code}}file upload{{code}} 377 -* //User message// (for upload back to the Core): “my workbench output, no additional sensitive data" 378 -* //Command~:// pilotcli file upload ./'Chemical Tracking Data rev.csv' -p indoctestproject/collaborator4 -z core -m "my workbench output, no additional sensitive data" 379 - 380 -When uploading data to the Core, you are reminded that you are bypassing the usual Green Room upload workflow. To confirm, type y at the prompt, or N to cancel. 381 - 382 -{{code language="none"}} 383 -collaborator4@jupyter-collaborator4:~$ pilotcli file upload ./'Chemical Tracking Data rev.csv' -p indoctestproject/collaborator4 -z core -m "my workbench output, no additional sensitive data" 384 -You are about to transfer data directly to the PILOT Core! In accordance with the PILOT Terms of Use, please confirm that you have made your best efforts to 385 -pseudonymize or anonymize the data and that you have the legal authority to transfer and make this data available for dissemination and use within the PILOT .If you 386 -need to process the data to remove sensitive identifiers, please cancel this transfer and upload the data to the Green Room to perform these actions. 387 -To cancel this transfer, enter [n/No] 388 -To confirm and proceed with the data transfer, enter [y/Yes] 389 - [y/N]: y 390 -Starting upload of: ./Chemical Tracking Data rev.csv 391 -Pre-upload complete. 392 -Uploading Chemical Tracking Data rev.csv: |██████████████████████████████ 100% 00:00 393 -Upload Time: 2.92s for 1 files 394 -All uploading jobs have finished. 395 -{{/code}} 396 - 397 -
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